rs2740566

chr7-99817782-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.789 in 152,138 control chromosomes in the GnomAD database, including 53,031 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.79 (53031 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.789 AC: 119945 AN: 152020 Hom.: 53028 Cov.: 31

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.912

Gnomad AMR AF: 0.885

Gnomad ASJ AF: 0.954

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.980

Gnomad FIN AF: 0.964

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.966

Gnomad OTH AF: 0.836

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.789 AC: 119971 AN: 152138 Hom.: 53031 Cov.: 31 AF XY: 0.796 AC XY: 59162 AN XY: 74354

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.886

Gnomad4 ASJ AF: 0.954

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.980

Gnomad4 FIN AF: 0.964

Gnomad4 NFE AF: 0.966

Gnomad4 OTH AF: 0.836

Alfa AF: 0.788 Hom.: 9764

Bravo AF: 0.762

Asia WGS AF: 0.943 AC: 3278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.050
Dann	Benign	0.70

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2740566; hg19: chr7-99415405;